I too have this problem.
Up until a year or so ago, any map I made was not given any cubemap VTFs. Then one day I noticed my maps were being given cubemapdefault.vtf and cubemapdefault.hdr.vtf.
Today I did an experiment and found that I was also being given a set of black cubemaps, one for each env_cubemap entity, including a set of black HDR cubemaps for a map that was only compiled in LDR.
I renamed the BSP and was able to build cubemaps in the game without a problem. I am wary of deleting content from a BSP using VIDE or Pakrat as I have heard it can cause corruption. I believe I may have experienced that myself in the past.
The strange happenings seemed to coincide with a great purge I had of all the downloaded content from my TF2 directory. At that same time I also noticed that the game engine now had a default cubemap of its own, where before I had never seen one, and all the documentation I had read insisted that TF2 was not shipped with its own set of default cubemaps. Yet they exist in the materials VPKs.
I believe I read something about a BSP not being writeable due to cubemaps that Hammer was including. Though it might have been some talk in the chat room. Since the default cubemaps do not take up much space you could try renaming your BSP after compile, and then buildcubemaps and pack custom content, ignoring the default cubemaps and leaving them there as a sort of vestigial organ. Static prop lighting may work correctly then as you won't be deleting anything from the BSP.
Some of the discussion on the web, including the thread you linked, mentions an altered version of VBSP for Source 2013 that stops the default cubemaps from being included. Perhaps that's worth a try?
Have you tried extracting all the VHV files from the BSP, and replacing them later, when you pack your new cubemap textures?
Another interesting point - I took one of my old, fully-detailed maps and saved it as a differently-named VMF. I compiled it on full HDR with the special prop lighting command arguments and the BSP was not given its own set of black cubemaps.
EDIT: I took the plunge and tried that modified vbsp.exe file but it doesn't work. Maybe it's too old for TF2's Hammer.